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In the Japanese version there are coins at the end of the last level in the Special World that spell out the words "YOU ARE SUPER PLAYER!!". This error was fixed in the Western localization, with the coins now spelling "YOU ARE A SUPER PLAYER!!"

In 1/92 interview with the game's producer Shigeru Miyamoto published in the edition of Famicom Tsuushin magazine, he was asked if the SNES version of Zelda be the same as the Super Famicom version. He responded that him and his team thought about making some improvements to the SNES version, including a number of things they could not complete in time for the Super Famicom release. Zelda makes full use of the available 8 MB of ROM space, but they knew they were going to need extra space for the English translation. They initially planned to increase the ROM size by 1 MB to solve this, until the compression routine their programmers wrote actually allowed them to fit everything in the original 8 MB storage. Miyamoto joked that they would save those aforementioned improvements for the next game.

In the western localiztion of the game, the Special World's levels are all named after 90's American surfer lingo, with the names being Gnarly, Tubular, Way Cool, Awesome, Groovy, Mondo, Outrageous, and Funky.

However in Japan the first two levels are named "Fun Course", third and fourth are named "Even the Mario Staff is Shocked Course", fifth and sixth are named "Specialists' Course", and seventh and eight are named "Championship Course". None of the shared names are even differentiated through numbers, like “Fun Course 1” or “Fun Course 2”.

In Hyrule Town, three travelers in the lobby of the Happy Hearth Inn, named Din, Nayru, and Farore, are the same characters as the Oracles from The Legend of Zelda: Oracle of Ages and Seasons. They are each looking for new homes to move into, which is the basis of an optional side quest that can be started after completing the Fortress of Winds. Gorman will now be renting out a house to tenants, and Link can convince one of the travelers to move in and obtain a Charm from that traveler. Afterwards, if Link fuses Kinstones with Bremor, Mutoh will become motivated to build a second house for Gorman to rent out. Link can then convince one of the remaining two travelers to move in, and will obtain their respective Charm. Each of the two houses built have a red roof and a blue roof, reflecting the color schemes of Din and Nayru respectively. However no third house can be built in the game, leaving the third Oracle homeless and stuck in the inn's lobby. In the European version of the game, Gorman makes a comment about wanting to build a house just south of the Royal Hyrule Library, on a plot of land occupied by cats, but he never does. This comment was removed from the North American release of the game which came out two months later.

Although the choice of who will remain homeless is entirely up to the player, the most probable canonical traveler to remain homeless is Farore. This is based on the lack of a green-roofed house to reflect her color scheme, her figurine description noting that she is bothered by people who "take advantage of her kind nature" (unlike Din and Nayru's descriptions which only point out where they are from and are looking for a new home), and by the development history of Oracle of Ages and Seasons, which was originally planned to be three games with each focusing on a different piece of the Triforce represented by a different Oracle, although only two games centering on Din and Nayru would ultimately be developed.

It's unknown if this incomplete side quest was an oversight, or if it was an intentional in-joke by Capcom, who developed both The Minish Cap and Oracle of Ages and Seasons.

The North American physical release of Metroid Prime: Remastered has reversible cover art. In the same way that the North American release's cover art was remade, the reversible cover art features a remake of the artwork used for the Japanese release of the original game. It's currently unknown if the Japanese physical release will feature reversible artwork from the North American release.

In the North American release, the cover art is reversible, with the back side featuring a map of Haven City. The front of the game's manual points this map out as a tip to players, but it should be noted that the Greatest Hits re-release of the game did not include this map, with the manual not being updated to reflect this change.

In the North American release, the game came with a pin-up poster featuring a blonde woman using the pole holding up a BMX bike cushion to pole dance on. The size of the pin-up varies with each port of the game, with the GameCube version's being double the size of the rest as the back side of it features a map of the game's first area, The Bronx, NYC.

However, that's not the only pin-up to come with the North American release of the game. The cover art is reversible, and if you flip it over to the back side you will find a pin-up of a redheaded woman in lingerie sitting backwards on a BMX bike, with tattoos of logos for the game and for the AKA Acclaim brand on each of her buttocks.

In the Japanese release, Trotty, the pig who grew a third arm from being pushed into the contaminated pool in Jolly Roger's Lagoon, is altered to remove references to his deformity. Not only is the third arm edited out of his model, but his dialogue is also rewritten; instead of worrying about growing additional limbs, his concern is that the polluted water will damage his swim trunks and beach ball. In the Japanese version of the Xbox Live Arcade port, Trotty's third arm is restored, but his dialogue remains censored.

On September 8, 2022, the United Kingdom's Queen Elizabeth II died, starting a national mourning period of ten days. Rumors began to circulate that Nintendo had postponed a planned Nintendo Direct in response to the news. On September 12, the Direct was formally revealed to air worldwide the next day, although it was not livestreamed in the UK. Instead, it was published as an on-demand video on Nintendo UK's YouTube channel at a later time. This Direct featured the full title reveal for the then-untitled Sequel to The Legend of Zelda: Breath of the Wild, revealing the game's subtitle to be "Tears of the Kingdom". This lead to even more speculation that the poor timing of this subtitle being the name of one of Nintendo's most anticipated games at the time coinciding with the Queen's death was what resulted in the Direct being delayed, rather than doing so purely out of respect. It wouldn't be until October 3 for Nintendo UK to begin their own promotion of the game, long after the mourning period ended and the Queen had been interred.

In the later-released Japanese version, Heart Blocks were added to Beanbean Castle Sewers, Oho Oasis, and Teehee Valley; these blocks fully restore Mario and Luigi's HP and BP at no cost. These blocks also feature in the 3DS remake across all regions, as the remake is based on the Japanese version of the original game.

In a Japan-exclusive guidebook published by Nintendo and Ape Inc., there is artwork depicting Link praying before a Crucifix, contrasting the game's origin story of the three Golden Goddesses, but also fitting with the Japanese version of the game calling the Sanctuary a Church. The Church's name was changed to the Sanctuary outside of Japan, presumably due to Nintendo's international policy on religious imagery, although this artwork and the rest featured in this guidebook were never republished internationally as other publishers released their own guides instead.

Due to South Korea banning casino gambling in video games, two of the minigames in "Bowser's Pinball Machine" were reworked. The Jackpot and Roulette minigames were changed to UFO and Whac-A-Mole minigames respectively.

The US version changed some plot details, most notably in how many kings are involved: while the Japanese version mentions three kings named Kells (ケルス), Rude (ルード), and Phillip　(フィリップ), the English version changed nearly all of these to Edward (the exception being a mention of Kells near the beginning of the game). As the story is already extremely cryptic, this was likely done in an attempt to make things less confusing.

In the Japanese release, the player is able to use Dive on the deep water tiles in Team Aqua's hideout due to a programming oversight. Because these tiles were never intended to lead anywhere, diving in them simply teleports the player back to Petalburg City, the lowest-indexed map location in the game. In the international release, this error is fixed by disallowing the player from using Dive in the hideout.

This glitch is not present in Pokémon Ruby & Sapphire, because in those games, the entrance to the hideout is no longer accessible after obtaining the Mind Badge, which is required to use Dive in the overworld.

The Japanese FM Towns release of Monkey Island 2 is completely missing the so-called "cliffside puzzle" (which involves stealing a fish from a chef, trading the fish to a fisherman for a rod, and casting your line over a cliff, so a seagull appears and snatches the piece of the treasure map away).

At first, it was speculated this was either a bug (with one person going so far as to officially submit it as a bug for the ScummVM emulator in 2006) or censorship. But looking at the game's source code, the change was seemingly intentional, with additional lines of code being added to tell the program to skip the correct sequence of events.

When asked about this, even former developers and play testers couldn't explain or remember why. Recent consensus is that this was most probably because of a technical issue involving vertical scrolling (where if the screen moved up and down you couldn't have objects or animations on the screen at the same time or the game's script would break - and the cliffside "room" is the only room in the game to feature vertical scrolling).

The console release features short cutscenes that play after defeating a boss. The Super Famicon version features blood on the defeated boss' portrait whereas the Super Nintendo version has no blood. Depending on the portrait the blood was recolored to look like either saliva or tears, or it was completely removed.

In the Japanese version, Dōbutsu no Mori +, two of the NES games that the player could obtain were Gomoku Narabe and Mahjong. The international release respectively replaces these titles with Soccer and Excitebike.

The scene where Elliot Edward gets attacked by zombies is censored in the Japanese release. In the international version he loses his lower body and guts and entrails are visible, whereas in the Japanese release he still has his legs intact. Even in the CERO Z version of the game (the version with the highest possible rating) his death is still censored.

The title screen for an unreleased Japanese version of the game called "Super American Football" can be found in the game's data.

On the wall of Ashley's bedroom, you can find a poster of the previous game's Japanese box art, released under the title "Clock Tower 2", and featuring Jennifer. When examined, Alyssa remarks "This isn't a game!" in reference to it being localized outside Japan as the first Clock Tower game despite it being a sequel, since the actual first Clock Tower game was never released outside Japan.